9. Third Party Tools¶

Chromium
- Citation:
- Site: https://www.chromium.org
- Version: 95.0.4615.0
- License: Google-authored portion is released under the BSD license.
BEDTools
- Citation: Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841-842.
- Site: https://github.com/arq5x/bedtools2
- Version: 2.19.1
- License: GPLv2
Pilon
- Citation: Walker BJ et al. (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014 Nov 19;9(11):e112963.
- Site: https://github.com/broadinstitute/pilon
- Version: 1.23
- License: GPLv2 & MIT
R
- Citation: R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.
- Site: http://www.r-project.org/
- Version: 3.6.3
- License: GPLv2
R_Packages
- Custom built direcotry containing all the packages required to install R packages offline
- The majority of the packages were downloaded automatically using the following R commands.
# Function to get dependencies and imports for a given list of packages.
getPackages <- function(packs){ packages <- unlist( tools::package_dependencies(packs, available.packages(), which=c("Depends", "Imports"), recursive=TRUE) ) packages <- union(packs, packages) packages }
# Use the function by providing the names of the desired packages.
packages <- getPackages(c("packageName", "packageName2")) # For example #packages <- getPackages(c("MetaComp","gtable","gridExtra","devtools","phyloseq","webshot","plotly","shiny","DT","ape", "igraph", "vegan","BH","plogr","dplyr","ade4","codetools","iterators","foreach","gplots"))
# Download packages to current/desired directory.
download.packages(packages, destdir="./", type="source")
- The packages specific to bioconductor (‘phyloseq’, ‘Biobase’, ‘biomformat’, ‘rhdf5’, ‘BiocGenerics’, ‘Biostrings’, ‘multtest’,’S4Vectors’,’IRanges’,’XVector’,’Rhdf5lib’,’zlibbioc’) needed to be manually downloade from the site.
- stringi defaults to downloading icudt55I.zip from online, the following method, from their documentation, was used to build a custom stringi package to avoid connecting to the internet.:
  1. File the `git clone https://github.com/gagolews/stringi.git` command. 2. Edit the `.Rbuildignore` file and get rid of the `^src/icu55/data` line. 3. Run `R CMD build stringi_dir_name`.
# index the downloaded packages into PACKAGES files.
require(tools) write_PACKAGES('.')
MetaComp: EDGE Taxonomy Assignments Visualization
- Citation:
- Site: https://cran.r-project.org/
- Version: 1.0.2
- License: BSD 3-Clause
GNU_parallel
- Citation: O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47
- Site: http://www.gnu.org/software/parallel/
- Version: 20190422
- License: GPLv3
tabix
- Citation:
- Site: http://sourceforge.net/projects/samtools/files/tabix/
- Version: 0.2.6
- License: MIT/Expat License
Primer3
- Citation: Untergasser, A., et al. (2012) Primer3–new capabilities and interfaces, Nucleic acids research, 40, e115.
- Site: http://primer3.sourceforge.net/
- Version: 2.3.5
- License: GPLv2
SAMtools
- Citation: Li, H., et al. (2009) The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078-2079.
- Site: http://www.htslib.org/
- Version: 1.16.1
- License: MIT

FaQCs
- Citation: Chienchi Lo, PatrickS.G. Chain (2014) Rapid evaluation and Quality Control of Next Generation Sequencing Data with FaQCs. BMC Bioinformatics. 2014 Nov 19;15
- Site: https://github.com/LANL-Bioinformatics/FaQCs
- Version: 2.08
- License: GPLv3
Seqtk
- Citation: Heng Li https://github.com/lh3/seqtk
- Site: https://github.com/lh3/seqtk
- Version: 1.3
- License: MIT
NanoPlot
- Citation: De Coster W, et al.(2018) NanoPack: visualizing and processing long read sequencing data, Bioinformatics. 2018 Mar 14.
- Site: https://github.com/wdecoster/NanoPlot
- Version: 1.40.0
- License: GPLv3
Porechop
- Citation:
- Site: https://github.com/rrwick/Porechop
- Version: 0.2.4
- License: GPLv3
wigToBigWig
- Citation: Kent, W.J., et al. (2010) BigWig and BigBed: enabling browsing of large distributed datasets, Bioinformatics, 26, 2204-2207.
- Site: https://genome.ucsc.edu/goldenPath/help/bigWig.html#Ex3
- Version: 4
- License: Free for academic, nonprofit, and personal use. A license is required for commercial usage.
sratoolkit
- Citation:
- Site: https://github.com/ncbi/sra-tools
- Version: 3.0.0
- License: Public Domain
ea-utils
- Citation: Erik Aronesty (2011) ea-utils : “Command-line tools for processing biological sequencing data”
- Site: https://code.google.com/archive/p/ea-utils/
- Version: 1.1.2-537
- License: MIT License
Mambaforge (Python 3)
- Citation:
- Site: https://github.com/conda-forge/miniforge
- Version: 22.11.1-4
- License: 3-clause BSD

9.10. Amplicon Analysis¶

QIIME2
- Citation: Caporaso et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010 May;7(5):335-6
- Site: http://qiime2.org/
- Version: 2023.5
- License: BSD 3-Clause
DETEQT: Diagnostic targeted sequencing adjudication
- Citation: Conrad TA et al. (2019) Diagnostic targETEd seQuencing adjudicaTion (DETEQT): Algorithms for Adjudicating Targeted Infectious Disease Next-Generation Sequencing Panels.
- Site: https://github.com/LANL-Bioinformatics/DETEQT
- Version: 0.3.0
- License: GPLv3

9.11. RNA-Seq Analysis¶

PyPiReT: Pipeline for Reference based Transcriptomics.
- Citation:
- Site: https://github.com/mshakya/PyPiReT
- Version: 0.3.2
- License: GPLv3